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Sample GSM7975685

Query DataSets for GSM7975685

Status

Public on Dec 01, 2024

Title

coral adult, deep, rep2

Sample type

SRA

Source name

whole organism tissue

Organism

Stylophora pistillata

Characteristics

tissue: whole organism tissue
age: adult
treatment: deep native

Treatment protocol

SS samples were sampled from the shallow reef and grown on the shallow reef (5m). SD were sampled form the shallow reef and translocated to grow on the mesophotic reef (45m).

Growth protocol

Coral adult and planulae samples were taken from the natural reef. 8 day and 60 day samples were grown in situ, held in plastic settlement chambers.

Extracted molecule

total RNA

Extraction protocol

Quick-DNA/RNA Miniprep Plus Kit, Zymo Research. Samples for RNAseq all had an RNA integrity number (RIN) >7.7
Sequencing libraries were prepared using a standard in house mRNA-Seq protocol at The Crown Genomics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Israel. The polyA fraction (mRNA) was purified from 500 ng of total RNA per sample, followed by fragmentation and the generation of double-stranded cDNA. Unique molecular identifiers were added prior to PCR amplification steps to reduce errors and quantitative bias introduced by amplification.
150 bp paired-end reads were sequenced on an Illumina NovaSeq SP with 100 cycles.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

Ad77

Data processing

All read processing was conducted using the HIVE computer cluster at the University of Haifa, Israel.
Read quality was assessed with FastQC and compiled with MultiQC. Adapters were removed from the reads using Cutadapt (Martin, 2011) and reads with a quality score of less than 25 were discarded using Trimmomatic (Bolger et al., 2014).
Reads were then aligned to the S. pistillata host genome assembly (NCBI GCA_002571385.1) using Star (Dobin et al., 2013). MultiQC was then repeated; percentage successful alignment was 81.55 ± 0.07 % (mean ± standard deviation).
Differential expression analysis was conducted on the genome-mapped reads using DEseq2 (Love et al., 2014) based on host genes with ≥5 reads in ≥2 samples.
Assembly: NCBI GCA_002571385.1
Supplementary files format and content: RawGeneCounts.csv, comma separated file with raw gene counts for each sample; annotations for the gene ids can be found in DEG lisst-FPMvalues.xlsx
Supplementary files format and content: DEG lisst-FPMvalues.xlsx, excel file containing output FPM value and significance level for each gene identifed for pairwise comparison of all treatments. Merged with gene and protein ID.

Submission date

Dec 14, 2023

Last update date

Dec 01, 2024

Contact name

Jessica Bellworthy

Organization name

Haifa University

Street address

199 Aba Khoushy Ave

City

Haifa